Contacts of the strand formed by residues 106 - 118 (chain A) in PDB entry 1MWT
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLY 106 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103A THR* 2.7 38.2 + - - +
104A ASN 3.2 1.2 + - - -
105A TYR* 1.3 81.9 - - - +
107A ASN* 1.3 63.7 + - - -
314A ILE* 3.4 11.6 - - - +
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Residues in contact with ASN 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A ILE 3.4 4.9 - - - +
102A LYS* 3.3 44.8 - - + +
103A THR 4.2 1.4 + - - +
106A GLY* 1.3 76.0 - - - -
108A ILE* 1.3 65.0 + - - +
109A ASP* 4.1 4.1 + - + +
313A LEU 5.0 1.9 - - - +
314A ILE* 4.2 8.9 - - - +
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Residues in contact with ILE 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A LEU* 5.0 6.3 - - + -
99A TYR 4.4 1.8 - - - +
100A LYS* 3.0 8.5 - - - +
101A ILE* 2.8 59.6 + - + +
103A THR* 4.6 10.8 - - + -
107A ASN* 1.3 77.5 - - - +
109A ASP* 1.3 64.5 + - - +
110A ARG* 4.2 16.4 - - + +
133A ILE* 4.9 7.9 - - + -
134A PRO* 4.2 25.6 - - + -
299A VAL* 5.7 1.1 - - + -
313A LEU* 3.9 35.4 - - + +
314A ILE* 4.2 18.6 - - + -
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Residues in contact with ASP 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A GLN* 3.1 20.2 + - - -
99A TYR 3.7 1.6 - - - -
100A LYS* 3.1 37.5 + - - +
107A ASN* 4.1 4.3 + - + +
108A ILE* 1.3 76.5 - - - +
110A ARG* 1.3 63.6 + - - +
111A ASN* 5.1 0.9 - - - +
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Residues in contact with ARG 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A GLN* 3.3 8.9 + - - -
99A TYR* 2.8 40.3 + - - +
108A ILE* 4.0 10.1 - - + -
109A ASP* 1.3 78.7 - - - +
111A ASN* 1.3 67.3 + - - +
134A PRO* 3.3 32.5 + - + -
135A GLY* 4.5 1.4 - - - -
311A HIS* 3.3 40.8 + - - +
312A THR 5.3 5.1 + - - -
313A LEU* 3.6 29.2 - - - +
176B LYS* 6.1 0.2 - - - +
209B ASP* 3.9 17.2 + - - +
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Residues in contact with ASN 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A ALA 3.4 8.5 - - - +
98A GLN* 2.8 23.4 + - - +
109A ASP 5.1 0.5 - - - +
110A ARG* 1.3 82.5 + - - +
112A VAL* 1.3 64.3 + - - +
134A PRO* 4.6 2.3 - - - +
135A GLY* 5.4 2.4 + - - -
176B LYS* 3.3 31.6 + - + +
177B ASN* 5.5 4.7 + - - -
209B ASP* 5.7 0.9 - - - +
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Residues in contact with VAL 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A ILE* 4.9 0.7 - - + -
96A ASP* 3.8 8.3 - - - +
97A ALA* 2.9 34.0 + - + +
99A TYR* 3.4 30.1 - - + +
111A ASN* 1.3 76.9 - - - +
113A GLN* 1.3 66.2 + - - +
114A PHE* 3.3 29.2 - - + -
130A SER* 3.8 13.2 - - - +
134A PRO* 3.1 39.3 - - + -
135A GLY 5.0 0.4 - - - +
176B LYS* 4.8 4.0 + - - +
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Residues in contact with GLN 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A ARG* 2.9 58.5 + - + +
95A VAL 3.2 5.2 - - - -
96A ASP* 3.8 4.0 - - - +
112A VAL* 1.3 80.0 - - - +
114A PHE* 1.3 61.8 + - - +
115A ASN* 3.9 25.0 + - - +
128A ASP* 4.7 8.5 - - - +
130A SER* 5.6 5.9 - - - -
176B LYS* 4.8 12.2 - - - +
208B ASP* 4.5 12.0 - - - +
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Residues in contact with PHE 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A ILE* 4.6 9.0 - - + -
37A ILE* 3.6 30.3 - - + -
80A ILE* 3.8 34.8 - - + -
93A LYS 4.1 0.3 - - - +
94A ARG* 3.7 1.2 - - - +
95A VAL* 2.9 49.5 + - + +
97A ALA* 4.6 2.2 - - + -
99A TYR* 4.2 6.5 - + - -
112A VAL* 3.3 35.2 - - + -
113A GLN* 1.3 75.5 - - - +
115A ASN* 1.3 64.9 + - - +
116A PHE* 3.9 20.4 - + + -
125A LEU* 5.2 6.3 - - + -
130A SER 4.6 2.5 - - - -
131A VAL* 4.2 27.8 - - + -
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Residues in contact with ASN 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A LYS* 6.1 0.9 - - - -
93A LYS 3.7 2.9 - - - +
94A ARG* 4.3 11.8 - - - +
113A GLN* 3.9 33.3 + - - +
114A PHE* 1.3 77.5 - - - +
116A PHE* 1.3 68.5 + - - +
117A VAL* 5.9 1.3 - - + -
125A LEU* 3.7 4.2 - - - +
126A ASP* 2.8 50.7 + - + +
128A ASP* 4.8 9.1 + - - -
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Residues in contact with PHE 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A ILE* 3.5 52.3 - - + -
33A THR* 4.1 13.2 - - - -
34A ILE* 4.2 9.4 - - + -
92A LYS* 3.4 3.5 - - - +
93A LYS* 2.9 37.7 + - + +
95A VAL* 3.9 21.3 - - + -
114A PHE* 3.9 17.9 - + + -
115A ASN* 1.3 76.9 - - - +
117A VAL* 1.3 71.7 + - - +
123A TRP* 3.7 26.0 - - + -
124A LYS 3.2 22.0 - - - +
125A LEU* 3.8 26.7 - - + -
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Residues in contact with VAL 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A SER* 3.7 29.6 - - - -
52A ILE* 6.0 2.0 - - + -
91A ASN 3.2 14.1 - - - +
92A LYS* 4.3 13.5 - - + -
115A ASN* 5.5 1.3 - - + -
116A PHE* 1.3 80.6 - - - +
118A LYS* 1.3 64.3 + - - +
119A GLU* 3.5 13.0 + - - +
123A TRP* 3.6 5.6 - - - -
124A LYS* 2.9 28.9 + - - +
126A ASP* 4.7 16.2 - - + +
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Residues in contact with LYS 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A LYS 4.5 5.6 - - - +
91A ASN* 3.1 48.9 + - + +
117A VAL* 1.3 72.6 - - - +
119A GLU* 1.3 73.0 + - - +
121A GLY* 3.5 37.5 + - - +
122A MET* 3.6 10.9 - - - +
123A TRP* 3.6 23.5 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il